ini.rxUi {rxode2}

Ini block for rxode2/nlmixr models

Description

The ini block controls initial conditions for 'theta' (fixed effects), 'omega' (random effects), and 'sigma' (residual error) elements of the model.

Usage

## S3 method for class 'rxUi'
ini(x, ..., envir = parent.frame(), append = NULL)

## Default S3 method:
ini(x, ..., envir = parent.frame(), append = NULL)

ini(x, ..., envir = parent.frame(), append = NULL)

Arguments

x

expression

...

Other expressions for ini() function

envir

the environment in which unevaluated model expressions is to be evaluated. May also be NULL, a list, a data frame, a pairlist or an integer as specified to sys.call.

append

Reorder theta parameters. NULL means no change to parameter order. A parameter name (as a character string) means to put the new parameter after the named parameter. A number less than or equal to zero means to put the parameter at the beginning of the list. A number greater than the last parameter number means to put the parameter at the end of the list.

Details

The ini() function is used in two different ways. The main way that it is used is to set the initial conditions and associated attributes (described below) in a model. The other way that it is used is for updating the initial conditions in a model, often using the pipe operator.

'theta' and 'sigma' can be set using either <- or = such as tvCL <- 1 or equivalently tvCL = 1. 'omega' can be set with a ~ such as etaCL ~ 0.1.

Parameters can be named or unnamed (though named parameters are preferred). A named parameter is set using the name on the left of the assignment while unnamed parameters are set without an assignment operator. tvCL <- 1 would set a named parameter of tvCL to 1. Unnamed parameters are set using just the value, such as 1.

For some estimation methods, lower and upper bounds can be set for 'theta' and 'sigma' values. To set a lower and/or upper bound, use a vector of values. The vector is c(lower, estimate, upper). The vector may be given with just the estimate (estimate), the lower bound and estimate (c(lower, estimate)), or all three (c(lower, estimate, upper)). To set an estimate and upper bound without a lower bound, set the lower bound to -Inf, c(-Inf, estimate, upper). When an estimation method does not support bounds, the bounds will be ignored with a warning.

'omega' values can be set as a single value or as the values of a lower-triangular matrix. The values may be set as either a variance-covariance matrix (the default) or as a correlation matrix for the off-diagonals with the standard deviations on the diagonals. Names may be set on the left side of the ~. To set a variance-covariance matrix with variance values of 2 and 3 and a covariance of -2.5 use ~c(2, 2.5, 3). To set the same matrix with names of iivKa and iivCL, use iivKa + iivCL~c(2, 2.5, 3). To set a correlation matrix with standard deviations on the diagonal, use cor() like iivKa + iivCL~cor(2, -0.5, 3).

Values may be fixed (and therefore not estimated) using either the name fixed at the end of the assignment or by calling fixed() as a function for the value to fix. For 'theta' and 'sigma', either the estimate or the full definition (including lower and upper bounds) may be included in the fixed setting. For example, the following are all effectively equivalent to set a 'theta' or 'sigma' to a fixed value (because the lower and upper bounds are ignored for a fixed value): tvCL <- fixed(1), tvCL <- fixed(0, 1), tvCL <- fixed(0, 1, 2), tvCL <- c(0, fixed(1), 2), or tvCL <- c(0, 1, fixed). For 'omega' assignment, the full block or none of the block must be set as fixed. Examples of setting an 'omega' value as fixed are: iivKa~fixed(1), iivKa + iivCL~fixed(1, 2, 3), or iivKa + iivCL~c(1, 2, 3, fixed). Anywhere that fixed is used, FIX, FIXED, or fix may be used equivalently.

For any value, standard mathematical operators or functions may be used to define the value. For example, log(2) and 24*30 may be used to define a value anywhere that a number can be used (e.g. lower bound, estimate, upper bound, variance, etc.).

Values may be labeled using the label() function after the assignment. Labels are are used to make reporting easier by giving a human-readable description of the parameter, but the labels do not have any effect on estimation. The typical way to set a label so that the parameter tvCL has a label of "Typical Value of Clearance (L/hr)" is tvCL <- 1; label("Typical Value of Clearance (L/hr)").

rxode2/nlmixr2 will attempt to determine some back-transformations for the user. For example, CL <- exp(tvCL) will detect that tvCL must be back-transformed by exp() for easier interpretation. When you want to control the back-transformation, you can specify the back-transformation using backTransform() after the assignment. For example, to set the back-transformation to exp(), you can use tvCL <- 1; backTransform(exp()).

Value

ini block

Author(s)

Matthew Fidler

See Also

Other Initial conditions: zeroRe()

Examples

# Set the ini() block in a model
one.compartment <- function() {
  ini({
    tka <- log(1.57); label("Ka")
    tcl <- log(2.72); label("Cl")
    tv <- log(31.5); label("V")
    eta.ka ~ 0.6
    eta.cl ~ 0.3
    eta.v ~ 0.1
    add.sd <- 0.7
  })
  model({
    ka <- exp(tka + eta.ka)
    cl <- exp(tcl + eta.cl)
    v <- exp(tv + eta.v)
    d/dt(depot) = -ka * depot
    d/dt(center) = ka * depot - cl / v * center
    cp = center / v
    cp ~ add(add.sd)
  })
}

# Use piping to update initial conditions
one.compartment %>% ini(tka <- log(2))
one.compartment %>% ini(tka <- label("Absorption rate, Ka (1/hr)"))
# Move the tka parameter to be just below the tv parameter (affects parameter
# summary table, only)
one.compartment %>% ini(tka <- label("Absorption rate, Ka (1/hr)"), append = "tv")
# When programming with rxode2/nlmixr2, it may be easier to pass strings in
# to modify the ini
one.compartment %>% ini("tka <- log(2)")